Magnesium in PDB 6tis: Drosophila Gdp-Tubulin

The structure of Drosophila Gdp-Tubulin, PDB code: 6tis was solved by B.Gigant, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.00 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.588, 126.515, 250.241, 90, 90, 90
R / Rfree (%)	18.3 / 21.9

The binding sites of Magnesium atom in the Drosophila Gdp-Tubulin (pdb code 6tis). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Drosophila Gdp-Tubulin, PDB code: 6tis:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Drosophila Gdp-Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Drosophila Gdp-Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:56.7 occ:1.00 O A:HOH686 2.0 54.9 1.0 O1B A:GTP501 2.1 51.7 1.0 O1G A:GTP501 2.1 51.6 1.0 O A:HOH673 2.1 49.9 1.0 O A:HOH617 2.1 50.4 1.0 O A:HOH636 2.2 47.7 1.0 PB A:GTP501 3.2 51.5 1.0 PG A:GTP501 3.3 51.1 1.0 O3B A:GTP501 3.6 51.5 1.0 O3A A:GTP501 3.6 52.1 1.0 O2G A:GTP501 4.0 50.4 1.0 CB A:GLN11 4.0 51.1 1.0 NZ B:LYS252 4.1 62.8 1.0 OD1 A:ASP69 4.1 60.9 1.0 OE1 A:GLU71 4.1 69.5 1.0 OD2 A:ASP69 4.2 61.0 1.0 N A:GLN11 4.3 50.1 1.0 O1A A:GTP501 4.4 54.1 1.0 OD2 A:ASP98 4.4 59.4 1.0 O2B A:GTP501 4.5 52.4 1.0 O3G A:GTP501 4.5 51.1 1.0 PA A:GTP501 4.6 53.2 1.0 CG A:ASP69 4.6 60.6 1.0 CB A:ASP98 4.7 56.8 1.0 CA A:GLN11 4.8 50.7 1.0 O A:HOH603 4.8 72.3 1.0 NE2 A:GLN11 4.9 57.4 1.0 CG A:ASP98 5.0 58.0 1.0

Magnesium binding site 2 out of 2 in the Drosophila Gdp-Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Drosophila Gdp-Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:61.8 occ:1.00 O C:HOH680 1.9 61.7 1.0 O C:HOH617 2.0 56.2 1.0 O1G C:GTP501 2.0 55.0 1.0 O1B C:GTP501 2.1 59.2 1.0 O C:HOH612 2.2 52.3 1.0 O C:HOH610 2.2 53.9 1.0 PB C:GTP501 3.1 59.2 1.0 PG C:GTP501 3.2 55.5 1.0 O3B C:GTP501 3.5 57.8 1.0 O3A C:GTP501 3.5 60.9 1.0 NZ D:LYS252 4.0 66.0 1.0 O2G C:GTP501 4.0 54.2 1.0 CB C:GLN11 4.1 59.8 1.0 OD1 C:ASP69 4.2 64.5 1.0 O1A C:GTP501 4.3 62.5 1.0 N C:GLN11 4.3 58.0 1.0 OD2 C:ASP69 4.3 69.7 1.0 OD2 C:ASP98 4.4 63.9 1.0 O3G C:GTP501 4.4 54.6 1.0 O2B C:GTP501 4.4 59.8 1.0 PA C:GTP501 4.5 62.5 1.0 OE1 C:GLU71 4.6 90.7 1.0 OE2 C:GLU71 4.6 90.2 1.0 CD C:GLU71 4.7 87.2 1.0 CG C:ASP69 4.7 66.1 1.0 CB C:ASP98 4.8 60.8 1.0 NE2 C:GLN11 4.8 64.8 1.0 CA C:GLN11 4.8 58.1 1.0 CG C:ASP98 5.0 63.6 1.0

R.Ayukawa, S.Iwata, H.Imai, S.Kamimura, M.Hayashi, K.X.Ngo, I.Minoura, S.Uchimura, T.Makino, M.Shirouzu, H.Shigematsu, K.Sekimoto, B.Gigant, E.Muto. Gtp-Dependent Formation of Straight Tubulin Oligomers Leads to Microtubule Nucleation J.Cell Biol. 2021.
ISSN: ESSN 1540-8140
DOI: 10.1083/JCB.202007033